Hi, I'm trying to run cTAKES following the documentation [1], and even after getting an UMLS Account, the runctakesCVD loads with exception: "org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultCasTermAnnotator" failed", but the only error in the log is:
./bin/runctakesCVD.sh -desc desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml (...) 03 Sep 2017 22:00:37 INFO Chunker - Chunker model file: org/apache/ctakes/chunker/models/chunker-model.zip 03 Sep 2017 22:00:38 INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 03 Sep 2017 22:00:38 INFO ContextDependentTokenizerAnnotator - Finite state machines loaded. 03 Sep 2017 22:00:38 INFO AbstractJCasTermAnnotator - Using dictionary lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence 03 Sep 2017 22:00:38 INFO AbstractJCasTermAnnotator - Exclusion tagset loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN VBP VBZ WDT WP WPS WRB 03 Sep 2017 22:00:38 INFO AbstractJCasTermAnnotator - Using minimum term text span: 3 03 Sep 2017 22:00:38 INFO AbstractJCasTermAnnotator - Using Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml 03 Sep 2017 22:00:38 INFO DictionaryDescriptorParser - Parsing dictionary specifications: 03 Sep 2017 22:00:38 INFO UmlsUserApprover - Checking UMLS Account at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user <username>: .03 Sep 2017 22:00:39 ERROR UmlsUserApprover - UMLS Account at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser is not valid for user <username> with <password> Tunneling the connection I can see: POST /restful/isValidUMLSUser HTTP/1.1 User-Agent: Java/1.8.0_144 Host: uts-ws.nlm.nih.gov:80 Accept: text/html, image/gif, image/jpeg, *; q=.2, */*; q=.2 Connection: keep-alive Content-type: application/x-www-form-urlencoded Content-Length: 76 licenseCode=<license>&user=<username>&password=<password> HTTP/1.0 301 Moved Permanently Location: https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser Strict-Transport-Security: max-age=31536000; includeSubDomains; preload Server: BigIP Connection: Keep-Alive Content-Length: 0 Where instead of <licensecode>, <username> and <password> are used the valid entries from the https://uts.nlm.nih.gov/ account. and the runtakesCVD.sh is changed as: java -Dctakes.umlsuser=<username> \ -Dctakes.umlspw="<password>" \ -Dctakes.umlsvendor="<licensecode>" \ -Dctakes.umlsaddr="http://localhost:8080/restful/isValidUMLSUser"; \ -cp $CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/* \ -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml \ -Dswing.defaultlaf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel \ -Dawt.useSystemAAFontSettings=on \ -Dsun.java2d.dpiaware=true \ -Xms512M \ -Xmx3g \ org.apache.uima.tools.cvd.CVD "$@" Going to: https://uts.nlm.nih.gov/services/nwsSemanticNetwork, I see that the wsdl [2] (all WSDLs [3]) is no longer available. For this reason I wonder if the API is still supported. OS: archlinux Java: openjdk version "1.8.0_144" OpenJDK Runtime Environment (build 1.8.0_144-b01) OpenJDK 64-Bit Server VM (build 25.144-b01, mixed mode) Network: no-proxy UMLS Account: <licensecode>, <username>, <password> Regards, Alexandru Zbarcea [1] - https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide guide [2] - https://uts.nlm.nih.gov:443/restful/isValidUMLSUser?wsdl [3] - https://uts.nlm.nih.gov/services/nwsSemanticNetwork
